Variant report

Variant	rs12623394
Chromosome Location	chr2:190352703-190352704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC40A1-2	chr2:190351899-190352718	NONHSAT076053

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10166420	0.93[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10198663	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1157910	0.91[LWK][hapmap]
rs11678414	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12613876	0.80[AFR][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs12622720	0.93[ASN][1000 genomes]
rs12693539	0.87[ASN][1000 genomes]
rs12693540	0.93[ASN][1000 genomes]
rs13009912	0.93[ASN][1000 genomes]
rs13015207	0.87[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13032853	0.93[LWK][hapmap]
rs1356976	0.80[ASN][1000 genomes]
rs1520854	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs1520856	0.80[ASN][1000 genomes]
rs1520857	0.89[LWK][hapmap]
rs1520858	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1520866	0.91[ASN][1000 genomes]
rs1595749	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs16831454	0.91[ASN][1000 genomes]
rs1851104	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs1866605	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs1898971	0.93[ASN][1000 genomes]
rs1992295	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs2304702	0.89[ASN][1000 genomes]
rs2351934	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs4309611	0.97[ASN][1000 genomes]
rs4666775	0.91[ASN][1000 genomes]
rs4667281	0.91[LWK][hapmap]
rs4667284	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6434339	0.81[JPT][hapmap]
rs6434342	0.84[ASN][1000 genomes]
rs6434343	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs6738193	0.87[ASN][1000 genomes]
rs6747222	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs734859	0.93[ASN][1000 genomes]
rs744556	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745742	0.93[ASN][1000 genomes]
rs7574403	0.87[ASN][1000 genomes]
rs7576165	0.81[JPT][hapmap]
rs8179541	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs893407	0.93[ASN][1000 genomes]
rs893408	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12623394	PMS1	cis	parietal	SCAN
rs12623394	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190366200	Weak transcription	Ovary	ovary
2	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:190350800-190353000	Enhancers	Liver	Liver
5	chr2:190351600-190353000	Enhancers	Placenta	Placenta
6	chr2:190352200-190352800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:190352200-190353000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:190352600-190352800	Enhancers	Colon Smooth Muscle	Colon
9	chr2:190352600-190353000	Enhancers	Rectal Smooth Muscle	rectum

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